Fig 1.
Domain architecture of the CRY/PHR superfamily.
The conserved domains were identified by the Conserved Domains Database (CDD) tool [19]. The reference sequences are as follows. Animal CRY: Homo sapiens CRY1 (NP_004066); plant CRY: Arabidopsis thaliana CRY1 (NP_567341); CRY-DASH: Xenopus laevis (NP_001084438); (6–4) PHR: Danio rerio (NP_571863); CPD PHR: D. rerio CPD class II PHR (NP_957358). The DNA photolyase related domain and a FAD binding domain are shared by both CRY and PHR; whereas the C-terminal variable domain is only present in CRY but not in PHY.
Table 1.
Occurrence of the CRY/PHR genes in main taxa.
Fig 2.
Unrooted maximum-likelihood tree of the CRY/PHR homologs.
Maximum-likelihood probabilities and Bayesian posteriors of the node support below 0.5 are not shown. The values are the likelihoods and posteriors respectively. The CRY/PHR superfamily include 6 main subfamilies: animal CRY and (6–4) photolyases, CRY-DASH, plant PHR2, plant CRY and 2 classes of CPD photolyases (CPD class I and class II).
Table 2.
Results of the codon based positive selection tests by HyPhy.
Fig 3.
Group conserved residues identified by ConSurf.
Degrees of conservation in the protein subfamilies visualized with Chimera v.1.6.2 [48]. The numbers of upper row and black bars indicate the level of conservation (0–9), 0 being the lowest.
Table 3.
Maximum-likelihood and Bayesian time estimates for the nodes (Mya) (Fig 4).
Fig 4.
Maximum-likelihood tree with local clock of the RPB2 homologs.
Maximum-likelihood probabilities and Bayesian posteriors of the node support below 0.5 are not shown. The values are the likelihoods and posteriors respectively. The internal calibration points (CP1-CP6): CP1 corresponds to the origin of eutherians (113–95.3 Mya); CP2 is the divergence of birds and crocodile (250.4–235 Mya); CP3 is the split of the ray-finned fishes and tetrapods (421.75–416.1 Mya) and CP4 corresponded to the divergence of flies and mosquitos (295.4–238.5 Mya). CP5 estimated the origin time of Angiospermae (179–158 Mya) [48,87]. CP6 is the origin of Ascomycota about 500–650 Mya [49]. In addition, time of five evolutionary events were estimated (Node11-5). Time estimates was showed in Table 3.